Talk:CH391L/S12/Synthetic Cooperation

• Jeffrey E. Barrick 13:04, 15 April 2012 (EDT):I don't agree with this statement: "With natural, single populations, maintaining homeostasis is relatively simple, as members in the population typically do not out compete each other, nor do they exhaust their supply of resources." Members in a population do compete with each other and they certainly exhaust their supply of resources in any overnight culture. More explanation needed.

• • Jeremy R. McLain 16:54, 15 April 2012 (EDT):I see what you mean. That idea came from the Brenner paper, where she cites two papers that refer to 'oral' microbial communities.[1][2] Looking at the this statement in the context of natural oral consortiums, it makes a little more sense because they obtain their resources when we consume food. I agree that they do compete with each other, however since they reach a steady state, none of the communities have out competed the others. I'll rephrase the statement to put it into the correct context and add those citations to the wiki.

• Jeffrey E. Barrick 13:04, 15 April 2012 (EDT):Too vague: What kinds of directed evolution, high-throughput screening, and gene-chip assay procedures will aid in design of consortia? For what purposes will these be used?

• • Jeremy R. McLain 17:31, 15 April 2012 (EDT):It is vague. The Brenner paper was outlining problems that need to be solved in order to better control the performance of consortium. They were pretty much just musing about what they would like to see in the future. So to put it more accurately, it's not necessarily "what kind" of techniques are used, just we need "better" techniques. The only way this is going to happen is with time and research.

• Jeffrey E. Barrick 13:04, 15 April 2012 (EDT):What were the conclusions of the Wintermute study? Evaluate their work.

• • Jeremy R. McLain 22:21, 15 April 2012 (EDT):The study found that 17% of the pair displayed synergistic growth, but that wasn't the point of the study. They wanted to characterize their results into a model that used "shadow prices" to represent the "cost" of releasing metabolites. This idea is apparently borrowed from linear programming models. I'll add another paragraph that goes into this idea a little bit.

• Jeffrey E. Barrick 13:04, 15 April 2012 (EDT):Is SMIT the same as CoSMO? Any salient differences?

• • Jeremy R. McLain 17:47, 15 April 2012 (EDT):From what I can tell, they are similar in that they characterize the interactions of two populations, however CoSMO is used specifically for "tailored" systems in which the metabolites produced by each strain are essential to the other. I suppose a SMIT system is composed of many CoSMO pairs, as well as other non-cooperative pairs.

• Jeffrey E. Barrick 13:04, 15 April 2012 (EDT):Typo: "Secrete" instead of "secret".

• • Jeremy R. McLain 17:47, 15 April 2012 (EDT):Fixed

• Jeffrey E. Barrick 13:04, 15 April 2012 (EDT):You have directly reproduced the figures AND captions from the Shou paper. The point of writing these topics is to evaluate and synthesize a topic, not verbatim reproduce what is already in a reference. I recommend only using very few selected figures (remember copyright discussion), and even then only portions of those figures where you are going to comment directly on what they were showing.

• • Jeremy R. McLain 18:03, 15 April 2012 (EDT):I removed the B section of the figure that showed the cartoon of the genes. The purpose of that figure is to show the necessity of adding another mutation that prevents the cell from using feedback inhibition when producing the metabolite.

• Jeffrey E. Barrick 13:04, 15 April 2012 (EDT):It's kind of surprising how few iGEM teams seem to have used consortia. I can't really find any others. Here's one for terraforming Mars, but they don't get as far as growing two different bacteria together.

• • Jeremy R. McLain 18:03, 15 April 2012 (EDT):I was initially going to use that project for this topic, but it seemed far too ridiculous to be a good "example." I suspect it's difficult enough to make something work with a single host and this difficulty is only compounded when we add the complexity of another organism and have to worry about competition, distribution of resources, etc.

• Brian Renda 12:19, 16 April 2012 (EDT):Heres that paper on spatially structured environments helping to stabilize synthetic consortia. [3] Do you think that this is a mandatory solution to dealing with consortia of organisms with vastly different fitnesses or can we design strategies to avoid loss of low-fitness populations through population fluctuations? One strategy might be to make systems not dependent on a single consortia, but dependent on the optimal function of independent competing consortia, to allow selection to favor the co-evolving group of organisms that best functions together.

• • Jeremy R. McLain 13:25, 16 April 2012 (EDT):In my opinion there's always a better way. I like the idea of of a "grey scale" when talking about dependence. So far I've noticed that the majority of consortiums are designed as "all or nothing" in terms of cooperation. Specifically, they are engineered such that if one of the populations is removed or dies off, a mass extinction occurs. I would like to see some systems that depend on each other, but not fully. This would allow evolution to do some of the design work for us, as you said.

• Midhat Patel 13:50, 16 April 2012 (EDT): Can you use simulations like these for directed evolution? For example, if you put different species with systems that use a specific carbon source with moderate efficiency and plated them on a media that contained primarily that carbon source, could you examine if and how those systems would evolve?

References

<biblio>

1. Marsh2006 pmid=12624191
2. Kuramitsu2007 pmid=18063722
3. Kim2008 pmid=19011107